Understanding water and nutrient utilization in agricultural layered soils is very important for improvement of agricultural management and protection of the environment. The objective of this paper was to determine the effect of layered soil profiles on crop yield and water and fertilizer nitrogen (N) utilization. Firstly, a water and nitrogen management model (WNMM) was calibrated and validated under a wheat-maize cropping system in an alluvial plain using published data of two soil profiles (named A and B). The results showed that the model can be used to simulate the water movement and N transport, as well as crop growth in the study area. Secondly, another three very different soil profiles (named C, D and E) near to profiles A and B were studied. Profile C had a silt loam-clay profile, profile D had a silty loam-clay-silt profile and profile E had a clay-silty loam-silt profile. The soil hydraulic parameters of these profiles were obtained by a Pedo-Transfer function using measured soil particle fraction. Given single and same set of initial conditions and field management practices, the WNMM was then used to simulate water and nitrogen balance and crop yield for the three profiles. Simulated results showed that the profiles (C, D and E) have similar water and fertilizer nitrogen (N) use efficiencies (WUE, FNUE) while the crop yields of profiles C and D were higher than that of profile E. Compared with profiles D and E, the profile C has least water drainage (127 mm) and total N loss (117 kg N ha−1). We concluded that layering of soil profiles has a strong effect on water and fertilizer nitrogen utilization and crop yield. Such affection led by layered character of soil profiles, therefore, needs to be taken into account in precision agriculture related researches.